病毒感染宿主细胞可能性的序列非比对法评估  

Evaluation of Infection Possibility of Host Cell by Virus on the Basis of Sequence Alignment-Free Comparison

作　　者：刘雪梅 臧翔 黄天来 杨哲 李文 叶宇中 胡珊[3] LIU Xue-mei1, ZANG Xiang1, HUANG Tian-lai1, YANG Zhe1,2 ,LI Wen1, YE Yu-zhong1 ,HU Shan3(1.School of Physics and Optoelectronics,South China University of Technology,Guangzhou 510640,Guangdong,China; 2.ICBC Guangzhou Dongcheng Branch，Guangzhou 510100,Guangdong,China; 3.Department of Biomedical Engineering,Zhongshan School of Medicine,Sun Yat-Sen University,Guangzhou 510275,Guangdong,Chin)

机构地区：[1]华南理工大学物理与光电学院,广东广州510640 [2]中国工商银行广州东城支行,广东广州510100 [3]中山大学中山医学院计算机中心,广东广州510275

出　　处：《华南理工大学学报（自然科学版）》2017年第11期106-111,共6页Journal of South China University of Technology(Natural Science Edition)

基　　金：国家自然科学基金青年基金资助项目(11205061;11205062)~~

摘　　要：病毒与宿主细胞在遗传信息上具有相似的字模式(k-tuple),病毒的DNA序列与其可感染的宿主细胞的DNA序列通过字模式的统计打分值往往比与随机宿主细胞的打分值高,也就是病毒和其可感染的宿主细胞的DNA序列有一定的相似性.基于此原理,文中利用序列非比对统计方法 D_2~S和D_2~*对病毒的DNA序列和宿主细胞的DNA序列基于字模式进行比对打分,将打分值与获得的阈值进行比较,判断该病毒是否能感染宿主细胞.实验结果表明,当k=5(k为字模式的的大小)、马尔可夫阶次为1时,D_2~S和D_2~*统计量均能较好地反映病毒与宿主细胞在基因上的相似性,而且通过ROC(受试者工作特征曲线)获得的最佳阈值可以作为一种判断病毒是否可感染宿主细胞的方法.A virus and its host cell have a similar word pattern（ k-tuple）. The scores of the DNA sequences of the virus and its host cell,which are obtained by means of the word pattern,are often higher than those of random host cells,that is to say,the DNA sequence of the virus is similar to that of its host. On the basis of this principle,two alignment-free statistics D_2~S and D_2~＊ are adopted to acquire the scores between the DNA sequence of the virus and that of its host cell in this paper. Then,the scores are compared with the threshold,so as to judge whether the virus can infect the host cell. Experimental results show that,when k = 5（ k is the size of k-tuple） and Markov order is 1,both of the statistics and can describe the similarity between the virus and its host cell in genes,and that the optimal threshold of D_2~S and D_2~＊ from the ROC（ Receiver Operator Characteristic） curves can be used to judge whether the virus can infect the host cell.

关 键 词：生物信息学 病毒 宿主细胞 序列非比对法 

分 类 号：Q71[生物学—分子生物学]